/**
* Copy from the copy method in StructUtil. Did not want to drag that code in. maybe this actually
* should go to struct.
*
* @param from
* @param to
* @param excludes
* @return
* @throws Exception
*/
public static <T extends struct> T xcopy(struct from, T to, String... excludes) throws Exception {
Arrays.sort(excludes);
for (Field f : from.fields()) {
if (Arrays.binarySearch(excludes, f.getName()) >= 0) continue;
Object o = f.get(from);
if (o == null) continue;
Field tof = to.getField(f.getName());
if (tof != null)
try {
tof.set(to, Converter.cnv(tof.getGenericType(), o));
} catch (Exception e) {
System.out.println(
"Failed to convert "
+ f.getName()
+ " from "
+ from.getClass()
+ " to "
+ to.getClass()
+ " value "
+ o
+ " exception "
+ e);
}
}
return to;
}
/**
* Method to convert a List of beans to a List of Array of Strings.
*
* @param beans the List of Beans.
* @param addNewHeader the new String Array for the Header row.
* @param <T> generic value.
* @return the List of Array of String content of the csv.
*/
@SuppressWarnings("unchecked")
public static <T> List<String[]> toStringArray(List<T> beans, String[] addNewHeader) {
List<String[]> records = new ArrayList<>();
// add header record
// records.add(new String[]{"ID","Name","Role","Salary"});
if (addNewHeader != null) records.add(addNewHeader);
for (T bean : beans) {
// beans.stream().map((bean) -> {
List<String> record = new ArrayList<>();
// invoke getter method and convert to String
Class<T> clazz = (Class<T>) bean.getClass();
// T t = ReflectionUtilities.invokeConstructor(clazz);
List<Method> getter = (List<Method>) ReflectionUtilities.findGetters(clazz, true);
for (Method method : getter) {
record.add(String.valueOf(ReflectionUtilities.invokeGetter(bean, method)));
}
// getter.stream().forEach((method) ->
// record.add(String.valueOf(ReflectionUtilities.invokeGetter(bean,method))));
// return record;
// }).forEach((record) -> records.add(ListUtilities.toArray(record)));
records.add(ListUtilities.toArray(record));
}
return records;
}
public T call() throws Exception {
final T result1 = step1.call();
if (result1.isSuccess() && !Thread.currentThread().isInterrupted()) {
return step2.call();
} else {
return result1;
}
}
public static <T> String fmtList(final List<T> list) {
String result = "";
for (T item : list) {
result += item.toString() + "\n";
}
return result;
}
@Override
public Tag copy() {
ListTag<T> res = new ListTag<T>(getName());
res.type = type;
for (T t : list) {
@SuppressWarnings("unchecked")
T copy = (T) t.copy();
res.list.add(copy);
}
return res;
}
public <T> void logMany(final PrintStream stream, final Collection<T> list) {
final String[] a = new String[list.size()];
int i = 0;
for (T e : list) {
a[i++] = e.toString();
}
Arrays.sort(a);
for (String o : a) {
stream.println(o);
}
}
/**
* @throws OSStatusException
* @since Available in iOS 2.0 and later.
*/
public <T extends Struct<T>> T getProperty(Struct<?> specifier, Class<T> type)
throws OSStatusException {
T data = Struct.allocate(type);
IntPtr dataSize = new IntPtr(Struct.sizeOf(data));
OSStatus status =
getProperty0(
this,
specifier == null ? 0 : Struct.sizeOf(specifier),
specifier == null ? null : specifier.as(VoidPtr.class),
dataSize,
data.as(VoidPtr.class));
OSStatusException.throwIfNecessary(status);
return data;
}
// insertion sort (n^2) ///bien
public int InsertionSort(T a[]) {
int comparaciones = 0;
for (int i = 1; i < a.length; i++) {
T aux = a[i];
int j = i - 1;
comparaciones++;
while (j >= 0 && aux.compareTo(a[j]) < 0) {
a[j + 1] = a[j]; // haces el hueco para insercion
j--;
}
a[j + 1] = aux; // insertas elemento
}
return comparaciones;
}
public String[] datosAleatorios(T[] a, int tamaño) {
ArrayList<String> aux = new ArrayList();
String[] b = new String[tamaño];
Random rnd = new Random();
int i = 0;
T elem = a[rnd.nextInt(a.length)];
while (i < tamaño) {
if (!aux.contains(elem.toString())) {
aux.add(elem.toString());
i++;
}
elem = a[rnd.nextInt(a.length)];
}
return aux.toArray(b);
}
public <T> String post(String resource, T object)
throws JAXBException, CloudException, InternalException {
StringWriter stringWriter = new StringWriter();
JAXBContext jc = JAXBContext.newInstance(object.getClass());
Marshaller m = jc.createMarshaller();
m.marshal(object, stringWriter);
return post(provider.getContext().getAccountNumber(), resource, stringWriter.toString());
}
/**
* This function returns a map whose entries hold the coordinates of the sequence as keys and the
* coordinates of the target sequences as values.</br> If a coordinate in sequence corresponds to
* a gap in another sequence, then -1 is assigned to that position.</br> For example suppose we
* have the sequences:</br> seq1: AAT-GCT-TCG</br> seq2: G--C-CTCT-C</br> seq3: A-T--GT-AG-</br>
* Then, if we wish to find the mapping of seq1's coordinates to seq2's coordinates, this will
* give us: 0 -> 0, 1 -> -1, 2 -> -1, 3 -> -1, 4 -> 2, 5 -> 3, 6 -> 5, 7 -> -1, 8 -> 6.</br> Also,
* if we wish to find the mapping of seq1's coordinates to seq2's and seq3's coordinates, this
* will give us: 0 -> {0, 0}, 1 -> {-1, -1}, 2 -> {-1, 1}, 3 -> {-1, -1}, 4 -> {2, 2}, 5 -> {3,
* 3}, 6 -> {5, 4}, 7 -> {-1, 5}, 8 -> {6, -1}.
*
* @param <T> This could be either the serial number of the sequence (valid range: [0,
* sequences.length-1]) or the sequence names
* @param <E>
* @param seqID The sequence ID (either serial number or name) which we wish to map</br> Note that
* the valid range of serial numbers is [0, sequences.length-1]
* @param targetSeqIDs The (target) sequences IDs (either serial numbers or names)
* @return A map whose keys are the sequence coordinates and values the corresponding coordinates
* of the target sequences
* @throws IllegalArgumentException
* @see GappedAlignmentString
*/
public <T extends Object> Map mapSeqCoords2SeqsCoords(
T generic_seqID, Vector<T> generic_targetSeqIDs)
throws IllegalArgumentException, IndexOutOfBoundsException {
GappedAlignmentString gas_seq;
GappedAlignmentString[] gas_targetSeqs;
String[] speciesNames = species();
// Check if generic_seqID is mistakenly included in the generic_targetSeqIDs set
if (generic_targetSeqIDs.contains(generic_seqID)) generic_targetSeqIDs.remove(generic_seqID);
if (generic_targetSeqIDs.size() + 1 > speciesNames.length)
throw new IndexOutOfBoundsException("You entered more sequences than are in the file.");
Map map = new HashMap();
// Check whether sequence IDs are inputed as serial numbers or as names
String seqsClassName = generic_seqID.getClass().getSimpleName();
// if( generic_seqID.getClass() instanceof java.lang.Integer )
// System.out.println("XAXA");
if (seqsClassName.equals("Integer")) {
Integer seqID = (Integer) generic_seqID;
Integer[] seqIDs = generic_targetSeqIDs.toArray(new Integer[generic_targetSeqIDs.size()]);
if ((StatUtil.findMax(seqIDs).getFirst() > speciesNames.length - 1)
|| (StatUtil.findMin(seqIDs).getFirst() < 0))
throw new IndexOutOfBoundsException(
"The sequence IDs (aka, serial numbers have to lie inside"
+ " the range 0 to speciesNames.length -1");
gas_seq = getGappedAlignment(speciesNames[seqID]);
gas_targetSeqs = new GappedAlignmentString[seqIDs.length];
for (int i = 0; i < seqIDs.length; i++)
gas_targetSeqs[i] = getGappedAlignment(speciesNames[seqIDs[i]]);
} else if (seqsClassName.equals("String")) {
String seqID = (String) generic_seqID;
String[] seqIDs = generic_targetSeqIDs.toArray(new String[generic_targetSeqIDs.size()]);
gas_seq = getGappedAlignment(seqID);
gas_targetSeqs = new GappedAlignmentString[seqIDs.length];
for (int i = 0; i < seqIDs.length; i++) gas_targetSeqs[i] = getGappedAlignment(seqIDs[i]);
} else {
throw new IllegalArgumentException("Sequence IDs should be either of type Integer or String");
}
// Pairwise Alignment
if (gas_targetSeqs.length == 1) {
map = doMapSeq2Seq(gas_seq, gas_targetSeqs);
}
// Multiple Alignment
else {
map = doMapSeq2Seqs(gas_seq, gas_targetSeqs);
}
return map;
} // end of mapSeqCoords2SeqsCoords method
/**
* Make a copy of a writable object using serialization to a buffer.
*
* @param orig The object to copy
* @return The copied object
*/
public static <T extends Writable> T clone(T orig, Configuration conf) {
try {
@SuppressWarnings("unchecked") // Unchecked cast from Class to Class<T>
T newInst = ReflectionUtils.newInstance((Class<T>) orig.getClass(), conf);
ReflectionUtils.copy(conf, orig, newInst);
return newInst;
} catch (IOException e) {
throw new RuntimeException("Error writing/reading clone buffer", e);
}
}
/**
* Construct a client-side proxy that implements the named protocol, talking to a server at the
* named address.
*
* @param protocol protocol
* @param clientVersion client's version
* @param addr server address
* @param ticket security ticket
* @param conf configuration
* @param factory socket factory
* @param rpcTimeout max time for each rpc; 0 means no timeout
* @return the proxy
* @throws IOException if any error occurs
*/
@SuppressWarnings("unchecked")
public static <T extends VersionedProtocol> ProtocolProxy<T> getProtocolProxy(
Class<T> protocol,
long clientVersion,
InetSocketAddress addr,
UserGroupInformation ticket,
Configuration conf,
SocketFactory factory,
int rpcTimeout)
throws IOException {
T proxy =
(T)
Proxy.newProxyInstance(
protocol.getClassLoader(),
new Class[] {protocol},
new Invoker(addr, ticket, conf, factory, rpcTimeout, protocol));
String protocolName = protocol.getName();
try {
ProtocolSignature serverInfo =
proxy.getProtocolSignature(
protocolName, clientVersion, ProtocolSignature.getFingerprint(protocol.getMethods()));
return new ProtocolProxy<T>(protocol, proxy, serverInfo.getMethods());
} catch (RemoteException re) {
IOException ioe = re.unwrapRemoteException(IOException.class);
if (ioe.getMessage()
.startsWith(IOException.class.getName() + ": " + NoSuchMethodException.class.getName())) {
// Method getProtocolSignature not supported
long serverVersion = proxy.getProtocolVersion(protocol.getName(), clientVersion);
if (serverVersion == clientVersion) {
return new ProtocolProxy<T>(protocol, proxy, null);
}
throw new VersionMismatch(protocolName, clientVersion, serverVersion, proxy);
}
throw re;
}
}
/**
* Method use OpenCsv Library for
*
* @param clazz the Class of the Bean.
* @param fileInputCsv the File CSV to parse.
* @param separator the char separator.
* @param <T> the generic variable.
* @return the List of Bean parsed from the CSV file.
*/
public static <T> List<T> parseCSVFileAsList(Class<T> clazz, File fileInputCsv, char separator) {
try {
List<T> beans;
try ( // create CSVReader object
CSVReader reader = new CSVReader(new FileReader(fileInputCsv), separator)) {
beans = new ArrayList<>();
// read line by line
String[] record;
// skip header row
String[] headers = reader.readNext();
// read content
while ((record = reader.readNext()) != null) {
T t = ReflectionUtilities.invokeConstructor(clazz);
for (int i = 0; i < record.length; i++) {
String nameMethod = "set" + org.apache.commons.lang3.StringUtils.capitalize(headers[i]);
// invoke setter method
if (ReflectionUtilities.checkMethod(clazz, nameMethod)) {
ReflectionUtilities.invokeSetter(t, nameMethod, record[i]);
} else {
logger.warn(
"Not exists the Method with name:"
+ nameMethod
+ " on the Bean:"
+ t.getClass().getName());
}
}
beans.add(t);
}
}
return beans;
} catch (IOException e) {
logger.error(
"Can't parse the CSV file:" + fileInputCsv.getAbsolutePath() + " -> " + e.getMessage(),
e);
return new ArrayList<>();
}
}
/** Return the value of an enum of the given type. Prefix allows a shortened form of the enum */
@SuppressWarnings("unchecked")
public <T extends Enum<T>> T getEnum(String prop, String prefix, T dflt) {
Enum<?> v = dflt;
String s = getProperty(prop);
if (s == null || s.length() == 0) return dflt;
if (prefix != null && !s.startsWith(prefix)) s = prefix + s;
Object[] vals = dflt.getClass().getEnumConstants();
if (vals == null) return dflt;
for (int i = 0; i < vals.length; ++i) {
Enum<?> e = (Enum<?>) vals[i];
if (e.name().equalsIgnoreCase(s)) {
v = e;
break;
}
}
return (T) v;
}
@SuppressWarnings("unchecked")
public static <T extends JsonElement> T deepCopy(T from) {
if (from == null) {
throw new IllegalArgumentException("from must not be null");
}
if (from instanceof JsonObject) {
return (T) deepCopyObj((JsonObject) from);
}
if (from instanceof JsonArray) {
return (T) deepCopyArr((JsonArray) from);
}
if (from instanceof JsonNull) {
return (T) JsonNull.INSTANCE;
}
if (from instanceof JsonPrimitive) {
// Nulls and primitives are immutable
return from;
}
throw new AssertionError("Unknown element type " + from.getClass().getName());
}
public void add(T tag) {
type = tag.getId();
list.add(tag);
}
@UsedFromByteCode
public static <T> int hashCode(T elementType) {
return elementType == null ? Integer.MIN_VALUE : elementType.hashCode();
}
@UsedFromByteCode
public static <T> boolean notEquals(T t1, T t2) {
return t1 == null ? t2 != null : !t1.equals(t2);
}
public static <T> boolean areObjectsEqual(T a, T b) {
if (a == null) {
return b == null;
}
return a.equals(b);
}
public <T> T map(Object source, T target, Object mappingCase) {
if (source != null && target != null) map(source, target, target.getClass(), mappingCase);
return target;
}
public <T> T get(String path, Class<T> c) {
Log.d(TAG, "get " + path); // NON-NLS
File f = new File(getFullCachePath(path));
if (!f.exists()) {
Log.w(TAG, "file: " + f.toString() + " not exists"); // NON-NLS
return null;
}
T object;
try {
StringBuffer fileData = new StringBuffer();
BufferedReader reader = new BufferedReader(new FileReader(f));
char[] buf = new char[1024];
int numRead = 0;
while ((numRead = reader.read(buf)) != -1) {
String readData = String.valueOf(buf, 0, numRead);
fileData.append(readData);
}
reader.close();
String json = fileData.toString();
Log.d(TAG, "cache: " + json); // NON-NLS
object = getGson().fromJson(json, c);
} catch (FileNotFoundException e) {
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (StreamCorruptedException e) {
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (IOException e) {
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (JsonSyntaxException e) {
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (IllegalArgumentException e) {
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (RuntimeException e) {
// не позволим кэшу убить нашу программу
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
} catch (Exception e) {
// не позволим кэшу убить нашу программу
Log.w(TAG, e.getMessage());
e.printStackTrace();
absoluteDelete(path);
return null;
}
if (object.getClass().toString().equals(c.toString())) return object;
else return null;
}
public void applyInputsToObject(Object obj) {
T config = this.getConfig();
if (config == null) {
return;
}
Field[] toObjectFields = obj.getClass().getSuperclass().getDeclaredFields();
Field[] fromObjectFields = config.getClass().getDeclaredFields();
for (int to = 0; to < toObjectFields.length; to++) {
String inputToName = toObjectFields[to].getName();
// Only input starting fields are used in configuration file
if (inputToName.startsWith("input")) {
for (int from = 0; from < fromObjectFields.length; from++) {
String inputFromName = fromObjectFields[from].getName();
if (toObjectFields[to].getType() == fromObjectFields[from].getType()
&& inputFromName.compareTo(inputToName) == 0) {
try {
if (toObjectFields[to].getType() == Calendar.class
&& inputToName.compareTo("inputEndingDate") == 0) {
Calendar currentDate = Calendar.getInstance();
toObjectFields[to].set(obj, currentDate);
continue;
}
toObjectFields[to].set(obj, fromObjectFields[from].get(config));
} catch (IllegalArgumentException ex) {
Logger.getLogger(ConfigLoader.class.getName()).log(Level.SEVERE, null, ex);
return;
} catch (IllegalAccessException ex) {
Logger.getLogger(ConfigLoader.class.getName()).log(Level.SEVERE, null, ex);
return;
}
}
}
}
}
toObjectFields = obj.getClass().getDeclaredFields();
fromObjectFields = config.getClass().getDeclaredFields();
for (int to = 0; to < toObjectFields.length; to++) {
String inputToName = toObjectFields[to].getName();
// Only input starting fields are used in configuration file
if (inputToName.startsWith("input")) {
for (int from = 0; from < fromObjectFields.length; from++) {
String inputFromName = fromObjectFields[from].getName();
if (toObjectFields[to].getType() == fromObjectFields[from].getType()
&& inputFromName.compareTo(inputToName) == 0) {
try {
if (toObjectFields[to].getType() == Calendar.class
&& inputToName.compareTo("inputEndingDate") == 0) {
Calendar currentDate = Calendar.getInstance();
toObjectFields[to].set(obj, currentDate);
continue;
}
toObjectFields[to].set(obj, fromObjectFields[from].get(config));
} catch (IllegalArgumentException ex) {
Logger.getLogger(ConfigLoader.class.getName()).log(Level.SEVERE, null, ex);
return;
} catch (IllegalAccessException ex) {
Logger.getLogger(ConfigLoader.class.getName()).log(Level.SEVERE, null, ex);
return;
}
}
}
}
}
}
/**
* Read an Enum value from DataInput, Enums are read and written using String values.
*
* @param <T> Enum type
* @param in DataInput to read from
* @param enumType Class type of Enum
* @return Enum represented by String read from DataInput
* @throws IOException
*/
public static <T extends Enum<T>> T readEnum(DataInput in, Class<T> enumType) throws IOException {
return T.valueOf(enumType, Text.readString(in));
}